BgeeCall: generate gene expression calls with BgeeCall

In BgeeCall: Automatic RNA-Seq present/absent gene expression calls generation

Description

BgeeCall allows to generate present/absent gene expression calls without using an arbitrary cutoff like TPM<1. Calls are generated based on reference intergenic sequences. These sequences are generated based on expression of all RNA-Seq libraries of each species integrated in Bgee (https://bgee.org).

Details

Thes most important functions are :

• generate_calls_workflow : generate present/absent calls on a computer

• generate_slurm_indexes : generate kallisto indexes for a list of libraries on a cluster with slurm queuing system.

• generate_slurm_calls : generate present/absent calls for a list of libraries on a cluster with slurm queuing system. Indexes have to be generated first with the function 'generate_slurm_indexes'

For more details please have a look at the vignette with the command vignette("BgeeCall")

Author(s)

Julien Wollbrett

See Also

https://github.com/BgeeDB/BgeeCall

BgeeCall documentation built on Dec. 12, 2020, 2 a.m.